The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins

RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two compleme...

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Published inNature communications Vol. 13; no. 1; pp. 2883 - 18
Main Authors Chu, Liang-Cui, Arede, Pedro, Li, Wei, Urdaneta, Erika C., Ivanova, Ivayla, McKellar, Stuart W., Wills, Jimi C., Fröhlich, Theresa, von Kriegsheim, Alexander, Beckmann, Benedikt M., Granneman, Sander
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 24.05.2022
Nature Publishing Group
Nature Portfolio
Subjects
38
38/70
38/91
45
45/23
45/88
631/326/41
631/326/421
631/337/475
631/45/500
82/29
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Bacteria
Bacterial Proteins - metabolism
Binding
Deoxyribonucleic acid
DNA
DNA - metabolism
DNA-Binding Proteins - metabolism
Drug resistance
Gene expression
Gram-positive bacteria
Helix-Turn-Helix Motifs - genetics
Humanities and Social Sciences
Metabolism
Methicillin
Methicillin-Resistant Staphylococcus aureus - genetics
Methicillin-Resistant Staphylococcus aureus - metabolism
multidisciplinary
Post-transcription
Protein Binding
Proteins
Proteome - metabolism
Proteomes
Ribonucleic acid
RNA
RNA - metabolism
RNA-binding protein
Science
Science (multidisciplinary)
Staphylococcus aureus
Staphylococcus infections
Transcription factors
Transcription Factors - metabolism
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Abstract RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs. RNA-binding proteins play key roles in controlling gene expression in many organisms. Here, Chu et al. identify hundreds of RNA-binding proteins in methicillin-resistant Staphylococcus aureus , and show that a major transcription factor uses its helix-turn-helix domain to bind RNAs near intrinsic transcription terminators.
AbstractList RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.
RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs. RNA-binding proteins play key roles in controlling gene expression in many organisms. Here, Chu et al. identify hundreds of RNA-binding proteins in methicillin-resistant Staphylococcus aureus , and show that a major transcription factor uses its helix-turn-helix domain to bind RNAs near intrinsic transcription terminators.
RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.
RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.RNA-binding proteins play key roles in controlling gene expression in many organisms. Here, Chu et al. identify hundreds of RNA-binding proteins in methicillin-resistant Staphylococcus aureus, and show that a major transcription factor uses its helix-turn-helix domain to bind RNAs near intrinsic transcription terminators.
RNA-binding proteins play key roles in controlling gene expression in many organisms. Here, Chu et al. identify hundreds of RNA-binding proteins in methicillin-resistant Staphylococcus aureus, and show that a major transcription factor uses its helix-turn-helix domain to bind RNAs near intrinsic transcription terminators.
RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.
ArticleNumber 2883
Author Wills, Jimi C.
Chu, Liang-Cui
Arede, Pedro
Urdaneta, Erika C.
Beckmann, Benedikt M.
Granneman, Sander
Li, Wei
von Kriegsheim, Alexander
Fröhlich, Theresa
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McKellar, Stuart W.
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PublicationYear 2022
Publisher Nature Publishing Group UK
Nature Publishing Group
Nature Portfolio
Publisher_xml – name: Nature Publishing Group UK
– name: Nature Publishing Group
– name: Nature Portfolio
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Snippet RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in...
RNA-binding proteins play key roles in controlling gene expression in many organisms. Here, Chu et al. identify hundreds of RNA-binding proteins in...
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SubjectTerms 38
38/70
38/91
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45/23
45/88
631/326/41
631/326/421
631/337/475
631/45/500
82/29
82/80
82/81
82/83
Bacteria
Bacterial Proteins - metabolism
Binding
Deoxyribonucleic acid
DNA
DNA - metabolism
DNA-Binding Proteins - metabolism
Drug resistance
Gene expression
Gram-positive bacteria
Helix-Turn-Helix Motifs - genetics
Humanities and Social Sciences
Metabolism
Methicillin
Methicillin-Resistant Staphylococcus aureus - genetics
Methicillin-Resistant Staphylococcus aureus - metabolism
multidisciplinary
Post-transcription
Protein Binding
Proteins
Proteome - metabolism
Proteomes
Ribonucleic acid
RNA
RNA - metabolism
RNA-binding protein
Science
Science (multidisciplinary)
Staphylococcus aureus
Staphylococcus infections
Transcription factors
Transcription Factors - metabolism
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Title The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins
URI https://link.springer.com/article/10.1038/s41467-022-30553-8
https://www.ncbi.nlm.nih.gov/pubmed/35610211
https://www.proquest.com/docview/2668568359
https://www.proquest.com/docview/2669502127
https://pubmed.ncbi.nlm.nih.gov/PMC9130240
https://doaj.org/article/f87797381ee945be8b0d419db2e0c750
Volume 13
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